Kinetics of non-nucleoside reverse transcriptase inhibitor resistance-associated mutations in HIV-1 proviral cellular reservoirs in NNRTI-experienced persons

In the blood mononuclear cells of persons living with HIV (PLWHs) with a history of virological failure (VF), some viral strains, archived as proviral DNA, can harbor mutations conferring resistance to antiretrovirals. This single-center, retrospective study included French PLWHs older than 18 years with a history of VF on a non-nucleoside reverse transcriptase inhibitor (NNRTI)-containing regimen and at least one NNRTI resistance-associated mutation (RAM) detected by Sanger sequencing at the time of VF. Next-generation sequencing targeting the reverse transcriptase gene, in combination with proviral DNA quantification, was performed on at least one whole blood sample after years of virological suppression on other antiretroviral regimens. Multivariate analysis identified factors associated with NNRTI RAM persistence. In total, 79 PLWHs were included. Samples were collected after a median of 10 years of virological suppression and 16 years after VF. NNRTI RAMs were not detected in the DNA in 39% of patients, and persistence was associated with a higher proviral DNA load and a higher HIV-1 RNA level at the time of VF. The mutational viral load tended to decrease over time (as assessed in 62 people with two samples collected at 3-year intervals). In contrast to other mutations such as M184V and INSTI RAMs, NNRTI RAMs tended to persist within the HIV-1 DNA reservoir. However, clearance of these archived mutations from the cellular reservoir was observed in some cases (low proviral DNA load, short duration of viral replication, and low HIV RNA level while taking failing NNRTIs).